Java Overlay类代码示例

import ij.gui.Overlay; //导入依赖的package包/类
private void updateShapes(final ImagePlus imp) {

        lastSourceImage = imp;

        if (imp == null) {
            return;
        }

        // Prepare overlay
        final Overlay overlay = new Overlay();
        for (final Region region : regions) {

            final Area area = new Area();
            for (final SubRegion subRegion : region.getSubRegions()) {
                final Shape shape = ShapeUtils.toShape(subRegion.getRoi());
                area.add(new Area(shape));
            }
            final ShapeRoi roi = new ShapeRoi(area);
            roi.setStrokeColor(region.getColor());
            roi.setFillColor(region.getColor());
            roi.setName(region.getName());
            overlay.add(roi);
        }

        imp.setOverlay(overlay);
    }
 

import ij.gui.Overlay; //导入依赖的package包/类
protected void label(Overlay overlay) {
	NumberFormat nf = NumberFormat.getInstance();
	nf.setMaximumFractionDigits(2);
	nf.setMinimumFractionDigits(2);

	for (int n = 0; n < tool.cBeads.size(); n++) {

		CalibrationBead first = tool.cBeads.get(n);
		TextRoi text = new TextRoi(first.getU(), first.getV() - 20, "Bead "
		/*
		 * + tool.ids[n] + " (" + nf.format(first.getX()) + ", " +
		 * nf.format(first.getY()) + ", " + nf.format(first.getZ()) + " | "
		 * + nf.format(first.getU()) + ", " + nf.format(first.getV()) + ")"
		 */);
		overlay.add(text);

	}
}
 

import ij.gui.Overlay; //导入依赖的package包/类
protected void overlayBeads(ArrayList<PointND> listOfBeads1, double radius1) {
	Overlay overlay = new Overlay();

	Roi[] beadRois1 = new Roi[listOfBeads1.size()];
	for (int i = 0; i < listOfBeads1.size(); i++) {
		double x = listOfBeads1.get(i).get(0);
		double y = listOfBeads1.get(i).get(1);
		beadRois1[i] = new EllipseRoi(x - radius1, y - radius1,
				x + radius1, y + radius1, 1.0);
		overlay.add(new EllipseRoi(x - radius1, y - radius1, x + radius1, y
				+ radius1, 1.0));
	}
	// overlayMultipleRois(beadRois1);
	// label(overlay);
	currentImage.setOverlay(overlay);
	// this happens in the GUI
	// currentImage.setOverlay(overlay);
}
 

import ij.gui.Overlay; //导入依赖的package包/类
protected void overlayBeadsF(ArrayList<PointND> listOfBeads1, double radius1) {
	Overlay overlay = new Overlay();
	Roi[] beadRois1 = new Roi[listOfBeads1.size()];
	for (int i = 0; i < listOfBeads1.size(); i++) {
		if (listOfBeads1.get(i) != null) {
			double x = listOfBeads1.get(i).get(0);
			double y = listOfBeads1.get(i).get(1);
			beadRois1[i] = new EllipseRoi(x - radius1, y - radius1, x
					+ radius1, y + radius1, 1.0);
			overlay.add(new EllipseRoi(x - radius1, y - radius1, x
					+ radius1, y + radius1, 1.0));
		}
	}

	// overlayMultipleRois(beadRois1);
	currentImage.setOverlay(overlay);
	// this happens in the GUI
	// currentImage.setOverlay(overlay);
}
 

import ij.gui.Overlay; //导入依赖的package包/类
protected void overlayBeadsCB(ArrayList<CalibrationBead> listOfBeads1,
		double radius1) {
	Overlay overlay = new Overlay();
	overlay.setLabelColor(Color.RED);
	overlay.setFillColor(Color.RED);
	Roi[] beadRois1 = new Roi[listOfBeads1.size()];
	for (int i = 0; i < listOfBeads1.size(); i++) {
		double x = listOfBeads1.get(i).getU();
		double y = listOfBeads1.get(i).getV();
		beadRois1[i] = new EllipseRoi(x - radius1, y - radius1,
				x + radius1, y + radius1, 1.0);
		overlay.add(new EllipseRoi(x - radius1, y - radius1, x + radius1, y
				+ radius1, 1.0));
	}
	// overlayMultipleRois(beadRois1);
	label(overlay);
	currentImage.setOverlay(overlay);
	// this happens in the GUI
	// currentImage.setOverlay(overlay);
}
 

import ij.gui.Overlay; //导入依赖的package包/类
public static void addRoi(ImagePlus imp, int slice, PointRoi roi)
{
	if (imp != null && slice > 0 && slice <= imp.getStackSize())
	{
		imp.setSlice(slice);
		if (imp.getWindow() != null)
			imp.getWindow().toFront();

		if (roi != null)
		{
			//imp.setRoi(roi);

			if (imp.getStackSize() > 1)
				roi.setPosition(slice);
			Overlay o = new Overlay(roi);
			o.setStrokeColor(Color.green);
			imp.setOverlay(o);
		}
		else
		{
			imp.setOverlay(null);
		}
	}
}
 

import ij.gui.Overlay; //导入依赖的package包/类
/**
 * Instantiates a new worker.
 *
 * @param jobs
 *            the jobs
 * @param stack
 *            the stack
 * @param actualCoordinates
 *            the actual coordinates
 * @param fitConfig
 *            the fit config
 * @param maxCount
 *            the max count
 * @param o
 *            the o
 */
public Worker(BlockingQueue<Integer> jobs, ImageStack stack,
		TIntObjectHashMap<ArrayList<Coordinate>> actualCoordinates, FitConfiguration fitConfig, Overlay o)
{
	this.jobs = jobs;
	this.stack = stack;
	this.actualCoordinates = actualCoordinates;
	this.fitConfig = fitConfig.clone();
	this.gf = new Gaussian2DFitter(this.fitConfig);
	this.spotFilter = config.createSpotFilter();
	this.relativeIntensity = !spotFilter.isAbsoluteIntensity();

	fitting = config.getFittingWidth();
	// Fit window is 2*fitting+1. The distance limit is thus 0.5 pixel higher than fitting. 
	limit = fitting + 0.5;
	spotHistogram = new int[20];
	resultHistogram = new int[spotHistogram.length];
	neighbourHistogram = new int[3][spotHistogram.length];
	almostNeighbourHistogram = new int[3][spotHistogram.length];
	this.o = o;
	rampedScore = new RampedScore(lowerDistance, matchDistance);
	if (signalFactor > 0)
		signalScore = new RampedScore(lowerSignalFactor, signalFactor);
}
 

import ij.gui.Overlay; //导入依赖的package包/类
/**
 * Adds an ROI point overlay to the image using the specified colour
 * 
 * @param imp
 * @param list
 * @param color
 */
public static void addOverlay(ImagePlus imp, List<? extends Coordinate> list, Color color)
{
	if (list.isEmpty())
		return;

	Color strokeColor = color;
	Color fillColor = color;

	Overlay o = imp.getOverlay();
	PointRoi roi = (PointRoi) PointManager.createROI(list);
	roi.setStrokeColor(strokeColor);
	roi.setFillColor(fillColor);
	roi.setShowLabels(false);

	if (o == null)
	{
		imp.setOverlay(roi, strokeColor, 2, fillColor);
	}
	else
	{
		o.add(roi);
		imp.setOverlay(o);
	}
}
 

import ij.gui.Overlay; //导入依赖的package包/类
/** Performs actual projection using specified method. If handleOverlay,
adds stack overlay elements from startSlice to stopSlice to projection*/
public void doProjection(boolean handleOverlay) {
	doProjection();
	Overlay overlay = imp.getOverlay();
	if (handleOverlay && overlay!=null)
		projImage.setOverlay(projectStackRois(overlay));
}
 

import ij.gui.Overlay; //导入依赖的package包/类
/** Performs actual projection using specified method. If handleOverlay,
 adds stack overlay elements from startSlice to stopSlice to projection*/
public void doProjection(boolean handleOverlay) {
    doProjection();
    Overlay overlay = imp.getOverlay();
    if (handleOverlay && overlay!=null)
        projImage.setOverlay(projectStackRois(overlay));
}
 

import ij.gui.Overlay; //导入依赖的package包/类
@Override
public void run(String arg) {
	ImagePlus imp = IJ.getImage();
	if (imp == null)
		return;

	Overlay overlay = imp.getOverlay();
	if (overlay == null || overlay.size() == 0) {
		IJ.showMessage("No overlay found!");
		return;
	}

	QuPathGUI gui = QuPathGUI.getInstance();
	if (gui == null) {
		IJ.showMessage("QuPath viewer not found!");
		return;
	}

	GenericDialog gd = new GenericDialog("Send overlay to QuPath");
	gd.addChoice("Choose_object_type", new String[]{"Annotation", "Detection"}, "Detection");
	gd.addCheckbox("Include_measurements", false);
	gd.showDialog();
	if (gd.wasCanceled())
		return;
	typeChoice = gd.getNextChoice();
	boolean asDetection = "Detection".equals(typeChoice);
	includeMeasurements = gd.getNextBoolean();

	QuPathViewer viewer = gui.getViewer();
	ImageServer<BufferedImage> server = viewer.getServer();
	double downsample = IJTools.estimateDownsampleFactor(imp, server);
	PathObjectHierarchy hierarchy = gui.getViewer().getHierarchy();
	
	List<PathObject> pathObjects = createPathObjectsFromROIs(imp, overlay.toArray(), server, downsample, asDetection, includeMeasurements, -1, viewer.getZPosition(), viewer.getTPosition());
	if (!pathObjects.isEmpty()) {
		Platform.runLater(() -> hierarchy.addPathObjects(pathObjects, true));
	}
}
 

import ij.gui.Overlay; //导入依赖的package包/类
public static Overlay addPointsToOverlay(double[] xCoord, double[] yCoord, Overlay overlay, int slice, Color c, int markerType) {
    assert xCoord.length == yCoord.length;
    float[] xs = new float[xCoord.length];
    float[] ys = new float[yCoord.length];
    for(int i = 0; i < xCoord.length; i++) {
        xs[i] = (float) xCoord[i];
        ys[i] = (float) yCoord[i];
    }
    overlay.add(new MultiplePointsRoi(xs, ys, slice, c, markerType));
    return overlay;
}
 

import ij.gui.Overlay; //导入依赖的package包/类
private final Overlay getOverlay(Color overlayColor, float overlayWidth) {
        Roi[] rois = roiManager.getRoisAsArray();
        Overlay over = new Overlay();
        for (int j = 0; j < rois.length; j++) {
                Roi roi = rois[j];
                roi.setStrokeColor(overlayColor);
                roi.setStrokeWidth(overlayWidth);
                over.add(roi);
        }
        
        return over;
}
 

import ij.gui.Overlay; //导入依赖的package包/类
/**
 * Adds a new ROI to the overlay using the coordinates from start to end (non-inclusive)
 * 
 * @param x
 * @param y
 * @param slice
 * @param indices
 * @param o
 * @param start
 * @param end
 */
private void appendRoi(float[] x, float[] y, int[] slice, int[] indices, Overlay o, int start, int end)
{
	int p = end - start;
	float[] x2 = new float[p];
	float[] y2 = new float[p];
	for (int j = start, ii = 0; j < end; j++, ii++)
	{
		x2[ii] = x[indices[j]];
		y2[ii] = y[indices[j]];
	}
	PointRoi roi = new PointRoi(x2, y2, p);
	roi.setPosition(slice[indices[start]]);
	o.add(roi);
}
 

import ij.gui.Overlay; //导入依赖的package包/类
private void addToOverlay(Overlay o, Roi roi, boolean isHyperStack, int frame)
{
	if (isHyperStack)
		roi.setPosition(0, 0, frame);
	else
		roi.setPosition(frame);
	o.add(roi);
}